CreatePredAlphaCost pred_alpha2k alpha11 T0358.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0358.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0358.t06.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 20 dry6.5 25 dry8 15 dry12 5 \
	phobic_fit 3 \
	sidechain 3 \
	n_ca_c	5 bad_peptide 10 \
	bystroff 5 \
	soft_clashes 40  backbone_clashes 2 \
	break 100  \
	pred_alpha2k 2 \
	pred_alpha04 2 \
	pred_alpha06 2 \
	constraints 10 \
	hbond_geom 5 \
	hbond_geom_backbone 10 \
	hbond_geom_beta 50 \
	hbond_geom_beta_pair 100 \
	missing_atoms 1 \
	maybe_metal 0.1 \
	maybe_ssbond 0

// remove maybe_ssbond weight if protein known to be in reducing environment.
// remove maybe_metal weight if protein known to have disulfides or
//	known not to bind metal ions.

// Add the following for extra-cellular proteins:
#	known_ssbond 0.5	# and put ssbond command in constraints file

// For comparative modeling, increase weight of break and hbond_geom...

// put any constraints here, such as helix constraints, strand constraints,
//	sheet constraints, ssbonds, hbonds, or just arbitrary pairs of atoms.

//include T0358.dssp-ehl2.constraints
//include T0358.undertaker-align.sheets
include rr.constraints

Constraint F37.CB R42.CB -10. 7.0 14.0 0.5 //hopefully to bring the exposed regions on beta sheet closer together
Constraint L63.CB V41.CB -10. 7.0 14.0 4 //Will bring the exposed region of the helix closer to the beta sheets.
Constraint I67.CB I27.CB -10. 7.0 14.0 6


HelixConstraint (T0358)T2	(T0358)T23	8/ hopefully will fix the kink in this helix, and free the N terminus

constraint((T0358)L39.CA, (T0358)L63.CA) [> 3 = 7 < 10] w=3 //lowering the distance constraint between these two residues will hopefully bring the alpha sheet in closer contact with the beta sheets.
constraint((T0358)N64.CA, (T0358)L80.CA) [> 7 = 9 < 12] w=1 // Will keep the C-terminal helices closer together.

constraint((T0358)V20A.CA, (T0358)W50A.CA) [> 3 = 9 < 13] w=5

//from try11-opt2.sheets
SheetConstraint (T0358)Y24 (T0358)S25	(T0358)D43 (T0358)R42	hbond (T0358)S25	8
SheetConstraint (T0358)I27 (T0358)E30	(T0358)V41 (T0358)R38	hbond (T0358)T28	8
SheetConstraint (T0358)L39 (T0358)D43	(T0358)R51 (T0358)R47	hbond (T0358)V41	8

Constraint A52.CB A59.CB -10. 7.0 14.0 8


//from try18-opt2.helics
HelixConstraint (T0358)G62	(T0358)S70	5
HelixConstraint (T0358)R73	(T0358)H87	8